diff getfastaBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/getfastaBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/getfastaBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,36 +1,34 @@
-<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@">
     <description>use intervals to extract sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #if str( $fasta_source.fasta_source_selector ) == 'history':
-          #set $fasta_file = $fasta_source.fasta
-        #else
-          #set $fasta_file = $fasta_source.fasta_id.fields.path
-        #end if
-        bedtools getfasta
-        $name
-        $tab
-        $strand
-        $split
-        -fi '$fasta_file'
-        -bed '$input'
-        -fo '$output'
-]]>
-    </command>
+    <command><![CDATA[
+#if str($fasta_source.fasta_source_selector) == 'history':
+    #set $fasta_file = $fasta_source.fasta
+#else
+    #set $fasta_file = $fasta_source.fasta_id.fields.path
+#end if
+bedtools getfasta
+$name
+$tab
+$strand
+$split
+-fi '$fasta_file'
+-bed '$input'
+-fo '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <conditional name="fasta_source">
-            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
-                <option value="history" selected="True">History</option>
+            <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
+                <option value="history" selected="true">History</option>
                 <option value="preloaded">Server indexed files</option>
             </param>
             <when value="history">
-                <param name="fasta" format="fasta" type="data" label="Fasta file" />
+                <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
             </when>
             <when value="preloaded">
                <param name="fasta_id" type="select">
@@ -38,19 +36,17 @@
                </param>
             </when>
         </conditional>
-        <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
-            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
-            help="(-name)" />
-        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
-            label="Report extract sequences in a tab-delimited format instead of in FASTA format"
-            help="(-tab)" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
+            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
+        <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
+            label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Force strandedness"
-            help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
+            help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
         <expand macro="split" />
     </inputs>
     <outputs>
-        <data format="fasta" name="output">
+        <data name="output" format="fasta">
             <change_format>
                 <when input="tab" value="-tab" format="tabular" />
             </change_format>
@@ -72,8 +68,7 @@
             <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
@@ -87,7 +82,6 @@
 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>